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Question about CombineGVCFs results

Hello all,

I have a quick question about the results of an CombineGVCFs file while creating large background files. Prior to combining the files a region of the .gvcf file from HC looks like this.

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR070473 13 19408518 . A <NON_REF> . . END=19409266 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 13 19409267 . T <NON_REF> . . END=19409323 GT:DP:GQ:MIN_DP:PL 0/0:4:12:2:0,6,60 13 19409324 . C <NON_REF> . . END=19409400 GT:DP:GQ:MIN_DP:PL 0/0:15:42:8:0,24,299

If you noticed the first individual looks like this SRR070473, with a 0/0:0:0:0:0,0,0 recorded, but after combining the file in batches of 200, the same information will be recorded as no call.

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR070473 SRR070477 SRR070505 SRR070516 SRR070517 SRR070772 SRR070779 SRR070796 SRR0 13 19408518 . A <NON_REF> . . END=19408519 GT:DP:GQ:MIN_DP:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.

The issue I'm seeing is when you attempt to use GenotypeGVCFs I get the following an error similar to this if using the file containing no call notation.

##### ERROR MESSAGE: cannot merge genotypes from samples without PLs; sample ERR031932 does not have likelihoods at position 1:10929

Best Answer


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